Using 3D in traditional illustration
You can use the 2d image as a background looking through a camera set to the pixels you want the final render to be, and then manipulate the 3d objects in relation to the 2d image without affecting the 2d image shading. Once you have the 3d objects set up and textured as you want them to be, and have worked out your lighting, you can render the 3d using transparent film setting (cycles) or transparent instead of Sky render(Blender Internal).

If you want a hand painted look for your 3d, you might try texture painting the 3d objects in blender after unwrapping them and setting up an image texture at a high enough resolution to look consistent with your final photoshop render.The material you use can either be set Shadeless(blender internal) or use an Emission shader(Cycles) to avoid unwanted shadow, as you can paint in your own stylized shading on the objects. You can also paint on a ground plane that has a transparent alpha image texture, and just paint the shadow there if you want.

The possibilities are endless with how you can manipulate 3d and 2d together, so I leave that up to your own opinion and taste to guide you.